[{"publisher":"SIAM","quality_controlled":"1","oa":1,"page":"926-947","doi":"10.1137/18M1207272","date_published":"2019-07-16T00:00:00Z","date_created":"2019-08-04T21:59:21Z","isi":1,"year":"2019","day":"16","publication":"Multiscale Modeling and Simulation","author":[{"first_name":"Gero","full_name":"Friesecke, Gero","last_name":"Friesecke"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","last_name":"Kniely"}],"external_id":{"arxiv":["1808.04200"],"isi":["000487931800002"]},"article_processing_charge":"No","title":"New optimal control problems in density functional theory motivated by photovoltaics","citation":{"ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272","apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.04200","open_access":"1"}],"month":"07","intvolume":" 17","abstract":[{"lang":"eng","text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size."}],"oa_version":"Preprint","volume":17,"issue":"3","publication_identifier":{"issn":["15403459"],"eissn":["15403467"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"6762","department":[{"_id":"JuFi"}],"date_updated":"2023-09-05T15:05:45Z"},{"article_number":"9","external_id":{"arxiv":["1807.08986"]},"article_processing_charge":"No","author":[{"first_name":"Sorina","full_name":"Ionica, Sorina","last_name":"Ionica"},{"first_name":"Pınar","full_name":"Kılıçer, Pınar","last_name":"Kılıçer"},{"full_name":"Lauter, Kristin","last_name":"Lauter","first_name":"Kristin"},{"full_name":"Lorenzo García, Elisa","last_name":"Lorenzo García","first_name":"Elisa"},{"id":"be8d652e-a908-11ec-82a4-e2867729459c","first_name":"Maria-Adelina","full_name":"Manzateanu, Maria-Adelina","last_name":"Manzateanu"},{"first_name":"Maike","last_name":"Massierer","full_name":"Massierer, Maike"},{"full_name":"Vincent, Christelle","last_name":"Vincent","first_name":"Christelle"}],"title":"Modular invariants for genus 3 hyperelliptic curves","citation":{"mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","date_created":"2022-03-18T12:09:48Z","date_published":"2019-01-02T00:00:00Z","doi":"10.1007/s40993-018-0146-6","year":"2019","publication":"Research in Number Theory","day":"02","article_type":"original","type":"journal_article","keyword":["Algebra and Number Theory"],"status":"public","_id":"10874","department":[{"_id":"TiBr"}],"date_updated":"2023-09-05T15:39:31Z","main_file_link":[{"url":"https://arxiv.org/abs/1807.08986","open_access":"1"}],"scopus_import":"1","intvolume":" 5","month":"01","abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}],"oa_version":"Preprint","volume":5,"publication_status":"published","publication_identifier":{"eissn":["2363-9555"],"issn":["2522-0160"]},"language":[{"iso":"eng"}]},{"ec_funded":1,"issue":"1","volume":372,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"cd283b475dd739e04655315abd46f528","file_id":"7101","file_size":884469,"date_updated":"2020-07-14T12:47:49Z","creator":"dernst","file_name":"2019_CommMathPhys_Jeblick.pdf","date_created":"2019-11-25T08:11:11Z"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"intvolume":" 372","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.","lang":"eng"}],"department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:47:49Z","ddc":["510"],"date_updated":"2023-09-06T10:47:43Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7100","date_created":"2019-11-25T08:08:02Z","date_published":"2019-11-08T00:00:00Z","doi":"10.1007/s00220-019-03599-x","page":"1-69","publication":"Communications in Mathematical Physics","day":"08","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"OA fund by IST Austria","title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","external_id":{"isi":["000495193700002"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Jeblick","full_name":"Jeblick, Maximilian","first_name":"Maximilian"},{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69. doi:10.1007/s00220-019-03599-x","apa":"Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.","chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69."},"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"citation":{"chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5.","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","ieee":"R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000496526100010"],"pmid":["31712756"]},"author":[{"first_name":"Roman","last_name":"Skokan","full_name":"Skokan, Roman"},{"full_name":"Medvecká, Eva","last_name":"Medvecká","first_name":"Eva"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"first_name":"Stanislav","last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"first_name":"Karel","full_name":"Müller, Karel","last_name":"Müller"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"full_name":"Karady, Michal","last_name":"Karady","first_name":"Michal"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou"},{"full_name":"Janacek, Dorina P.","last_name":"Janacek","first_name":"Dorina P."},{"full_name":"Hammes, Ulrich Z.","last_name":"Hammes","first_name":"Ulrich Z."},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"PIN-driven auxin transport emerged early in streptophyte evolution","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"year":"2019","isi":1,"has_accepted_license":"1","publication":"Nature Plants","day":"01","page":"1114-1119","date_created":"2019-11-25T09:08:04Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1038/s41477-019-0542-5","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2023-09-06T11:09:49Z","ddc":["580"],"file_date_updated":"2020-10-14T08:54:49Z","department":[{"_id":"JiFr"}],"_id":"7106","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["2055-0278"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8660","checksum":"94e0426856aad9a9bd0135d5436efbf1","file_size":1980851,"date_updated":"2020-10-14T08:54:49Z","creator":"dernst","file_name":"2019_NaturePlants_Skokan_accepted.pdf","date_created":"2020-10-14T08:54:49Z"}],"ec_funded":1,"issue":"11","volume":5,"abstract":[{"text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 5","month":"11"},{"title":"Persistent and polarized global actin flow is essential for directionality during cell migration","external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"article_processing_charge":"No","author":[{"last_name":"Yolland","full_name":"Yolland, Lawrence","first_name":"Lawrence"},{"first_name":"Mubarik","last_name":"Burki","full_name":"Burki, Mubarik"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"full_name":"Luchici, Andrei","last_name":"Luchici","first_name":"Andrei"},{"first_name":"Fiona N.","full_name":"Kenny, Fiona N.","last_name":"Kenny"},{"last_name":"Davis","full_name":"Davis, John Robert","first_name":"John Robert"},{"full_name":"Serna-Morales, Eduardo","last_name":"Serna-Morales","first_name":"Eduardo"},{"first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","full_name":"Müller, Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Andrew","last_name":"Davidson","full_name":"Davidson, Andrew"},{"full_name":"Wood, Will","last_name":"Wood","first_name":"Will"},{"full_name":"Schumacher, Linus J.","last_name":"Schumacher","first_name":"Linus J."},{"first_name":"Robert G.","full_name":"Endres, Robert G.","last_name":"Endres"},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"last_name":"Stramer","full_name":"Stramer, Brian M.","first_name":"Brian M."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.","ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-11-25T08:55:00Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1038/s41556-019-0411-5","page":"1370-1381","publication":"Nature Cell Biology","day":"01","year":"2019","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"7105","department":[{"_id":"MiSi"}],"date_updated":"2023-09-06T11:08:52Z","intvolume":" 21","month":"11","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence."}],"issue":"11","volume":21,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]}},{"year":"2019","isi":1,"publication":"Journal of the ACM","day":"01","date_created":"2019-11-26T10:13:59Z","doi":"10.1145/3314024","date_published":"2019-06-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","citation":{"chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"article_processing_charge":"No","author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"last_name":"Patak","full_name":"Patak, Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"title":"Shellability is NP-complete","article_number":"21","publication_status":"published","publication_identifier":{"issn":["0004-5411"]},"language":[{"iso":"eng"}],"issue":"3","related_material":{"record":[{"id":"184","status":"public","relation":"earlier_version"}]},"volume":66,"abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1711.08436.pdf"}],"scopus_import":"1","intvolume":" 66","month":"06","date_updated":"2023-09-06T11:10:58Z","department":[{"_id":"UlWa"}],"_id":"7108","article_type":"original","type":"journal_article","status":"public"},{"oa":1,"quality_controlled":"1","publisher":"IEEE","publication":"2019 IEEE International Symposium on Information Theory","day":"01","year":"2019","isi":1,"date_created":"2019-11-28T10:19:21Z","date_published":"2019-07-01T00:00:00Z","doi":"10.1109/isit.2019.8849240","article_number":"8849240","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240.","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240."},"title":"Strong chain rules for min-entropy under few bits spoiled","external_id":{"arxiv":["1702.08476"],"isi":["000489100301043"]},"article_processing_charge":"No","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|XCell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966."},"title":"Defying gravity: a plant's quest for moisture","author":[{"first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"No","external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"publication_status":"published","volume":29,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content.","lang":"eng"}],"month":"12","intvolume":" 29","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41422-019-0254-4","open_access":"1"}],"date_updated":"2023-09-06T11:20:58Z","department":[{"_id":"JiFr"}],"_id":"7143","status":"public","article_type":"original","type":"journal_article"},{"abstract":[{"text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 5","publication_identifier":{"issn":["2056-6387"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7157","checksum":"13e0ea1d4f9b5f5710780d9473364f58","date_updated":"2020-07-14T12:47:50Z","file_size":1580132,"creator":"dernst","date_created":"2019-12-09T08:25:06Z","file_name":"2019_NPJ_Rueda.pdf"}],"language":[{"iso":"eng"}],"volume":5,"ec_funded":1,"_id":"7156","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-06T11:22:39Z","ddc":["530"],"department":[{"_id":"JoFi"}],"file_date_updated":"2020-07-14T12:47:50Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"npj Quantum Information","date_published":"2019-12-01T00:00:00Z","doi":"10.1038/s41534-019-0220-5","date_created":"2019-12-09T08:18:56Z","article_number":"108","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","grant_number":"732894"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105"}],"citation":{"ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5.","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” npj Quantum Information, vol. 5. Springer Nature, 2019.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez"},{"last_name":"Hease","full_name":"Hease, William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"external_id":{"isi":["000502996200003"],"arxiv":["1909.01470"]},"article_processing_charge":"No","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer"},{"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","author":[{"first_name":"Pilar","full_name":"Guerrero, Pilar","last_name":"Guerrero"},{"last_name":"Perez-Carrasco","full_name":"Perez-Carrasco, Ruben","first_name":"Ruben"},{"first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P"},{"full_name":"Page, David","last_name":"Page","first_name":"David"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"first_name":"Karen M.","full_name":"Page, Karen M.","last_name":"Page"}],"external_id":{"isi":["000507575700004"],"pmid":["31784457"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297."},"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"article_number":"dev176297","date_published":"2019-12-04T00:00:00Z","doi":"10.1242/dev.176297","date_created":"2019-12-10T14:39:50Z","day":"04","publication":"Development","has_accepted_license":"1","isi":1,"year":"2019","publisher":"The Company of Biologists","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"AnKi"}],"ddc":["570"],"date_updated":"2023-09-06T11:26:36Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7165","issue":"23","volume":146,"ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:50Z","file_size":7797881,"date_created":"2019-12-13T07:34:06Z","file_name":"2019_Development_Guerrero.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7177","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication_status":"published","month":"12","intvolume":" 146","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube.","lang":"eng"}]},{"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"title":"Deciding fast termination for probabilistic VASS with nondeterminism","external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"article_processing_charge":"No","author":[{"first_name":"Tomás","full_name":"Brázdil, Tomás","last_name":"Brázdil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Antonín","last_name":"Kucera","full_name":"Kucera, Antonín"},{"full_name":"Novotný, Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-12-15T23:00:44Z","doi":"10.1007/978-3-030-31784-3_27","date_published":"2019-10-21T00:00:00Z","page":"462-478","publication":"International Symposium on Automated Technology for Verification and Analysis","day":"21","year":"2019","isi":1,"status":"public","conference":{"location":"Taipei, Taiwan","end_date":"2019-10-31","start_date":"2019-10-28","name":"ATVA: Automated TEchnology for Verification and Analysis"},"type":"conference","_id":"7183","department":[{"_id":"KrCh"}],"date_updated":"2023-09-06T12:40:58Z","intvolume":" 11781","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1907.11010","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).","lang":"eng"}],"volume":11781,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030317836"],"eissn":["16113349"],"issn":["03029743"]}},{"ddc":["580"],"date_updated":"2023-09-06T14:33:46Z","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"JiFr"}],"_id":"7182","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"7185","checksum":"995aa838aec2064d93550de82b40bbd1","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-12-16T07:58:43Z","file_name":"2019_FrontiersPlant_Alcantara.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:52Z","file_size":1532505}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664462X"]},"publication_status":"published","volume":10,"issue":"11","oa_version":"Published Version","pmid":1,"abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"month":"11","intvolume":" 10","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437.","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437.","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437"},"title":"Systematic Y2H screening reveals extensive effector-complex formation","author":[{"full_name":"Alcântara, André","last_name":"Alcântara","first_name":"André"},{"first_name":"Jason","full_name":"Bosch, Jason","last_name":"Bosch"},{"first_name":"Fahimeh","full_name":"Nazari, Fahimeh","last_name":"Nazari"},{"last_name":"Hoffmann","full_name":"Hoffmann, Gesa","first_name":"Gesa"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"last_name":"Darino","full_name":"Darino, Martin A.","first_name":"Martin A."},{"full_name":"Olukayode, Toluwase","last_name":"Olukayode","first_name":"Toluwase"},{"last_name":"Reumann","full_name":"Reumann, Daniel","first_name":"Daniel"},{"full_name":"Baggaley, Laura","last_name":"Baggaley","first_name":"Laura"},{"last_name":"Djamei","full_name":"Djamei, Armin","first_name":"Armin"}],"article_processing_charge":"No","external_id":{"pmid":["31803201"],"isi":["000499821700001"]},"article_number":"1437","day":"14","publication":"Frontiers in Plant Science","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.3389/fpls.2019.01437","date_published":"2019-11-14T00:00:00Z","date_created":"2019-12-15T23:00:43Z","quality_controlled":"1","publisher":"Frontiers","oa":1},{"project":[{"name":"Modeling epithelial tissue mechanics during cell invasion","grant_number":"M02379","call_identifier":"FWF","_id":"264CBBAC-B435-11E9-9278-68D0E5697425"}],"article_number":"5516","author":[{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","last_name":"Akhmanova"},{"first_name":"Nataliia","full_name":"Konstantinova, Nataliia","last_name":"Konstantinova"},{"last_name":"Malínská","full_name":"Malínská, Kateřina","first_name":"Kateřina"},{"first_name":"Johannes","full_name":"Leitner, Johannes","last_name":"Leitner"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"}],"article_processing_charge":"No","external_id":{"pmid":["31797871"],"isi":["000500508100001"]},"title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","citation":{"ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","oa":1,"doi":"10.1038/s41467-019-13543-1","date_published":"2019-12-01T00:00:00Z","date_created":"2019-12-15T23:00:43Z","has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"Nature Communications","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7180","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"DaSi"}],"date_updated":"2023-09-06T14:08:21Z","ddc":["570"],"scopus_import":"1","month":"12","intvolume":" 10","abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":10,"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"creator":"dernst","file_size":5156533,"date_updated":"2020-07-14T12:47:52Z","file_name":"2019_NatureComm_Retzer.pdf","date_created":"2019-12-16T07:37:50Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7184","checksum":"77e8720a8e0f3091b98159f85be40893"}],"language":[{"iso":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470."},"title":"Large multiple sequence alignments with a root-to-leaf regressive method","author":[{"first_name":"Edgar","full_name":"Garriga, Edgar","last_name":"Garriga"},{"last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo","first_name":"Paolo"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"first_name":"Ionas","full_name":"Erb, Ionas","last_name":"Erb"},{"full_name":"Mansouri, Leila","last_name":"Mansouri","first_name":"Leila"},{"last_name":"Baltzis","full_name":"Baltzis, Athanasios","first_name":"Athanasios"},{"last_name":"Laayouni","full_name":"Laayouni, Hafid","first_name":"Hafid"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"full_name":"Notredame, Cedric","last_name":"Notredame","first_name":"Cedric"}],"article_processing_charge":"No","external_id":{"isi":["000500748900021"],"pmid":["31792410"]},"project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"01","publication":"Nature Biotechnology","isi":1,"year":"2019","date_published":"2019-12-01T00:00:00Z","doi":"10.1038/s41587-019-0333-6","date_created":"2019-12-15T23:00:43Z","page":"1466-1470","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-09-06T14:32:52Z","department":[{"_id":"FyKo"}],"_id":"7181","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"publication_status":"published","issue":"12","related_material":{"record":[{"relation":"research_data","status":"public","id":"13059"}]},"volume":37,"ec_funded":1,"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.","lang":"eng"}],"month":"12","intvolume":" 37","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}]},{"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas."}],"month":"11","intvolume":" 8","scopus_import":"1","file":[{"file_name":"2019_eLife_Llorca.pdf","date_created":"2020-02-18T15:19:26Z","file_size":2960543,"date_updated":"2020-07-14T12:47:53Z","creator":"dernst","checksum":"b460ecc33e1a68265e7adea775021f3a","file_id":"7503","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","volume":8,"ec_funded":1,"_id":"7202","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-09-06T14:38:39Z","department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:47:53Z","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"day":"18","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.7554/eLife.51381","date_published":"2019-11-18T00:00:00Z","date_created":"2019-12-22T23:00:42Z","article_number":"e51381","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381."},"title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","author":[{"first_name":"Alfredo","last_name":"Llorca","full_name":"Llorca, Alfredo"},{"first_name":"Gabriele","full_name":"Ciceri, Gabriele","last_name":"Ciceri"},{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wong","full_name":"Wong, Fong Kuan","first_name":"Fong Kuan"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","full_name":"Serafeimidou-Pouliou, Eleni","last_name":"Serafeimidou-Pouliou"},{"full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero","first_name":"Marian"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"last_name":"Meyer","full_name":"Meyer, Martin","first_name":"Martin"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Maravall","full_name":"Maravall, Miguel","first_name":"Miguel"},{"first_name":"Oscar","last_name":"Marín","full_name":"Marín, Oscar"}],"article_processing_charge":"No","external_id":{"isi":["000508156800001"],"pmid":["31736464"]}},{"title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"article_processing_charge":"No","author":[{"first_name":"Lisa","full_name":"Klotz, Lisa","last_name":"Klotz"},{"last_name":"Wendler","full_name":"Wendler, Olaf","first_name":"Olaf"},{"first_name":"Renato","last_name":"Frischknecht","full_name":"Frischknecht, Renato"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Holger","last_name":"Schulze","full_name":"Schulze, Holger"},{"last_name":"Enz","full_name":"Enz, Ralf","first_name":"Ralf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R."},"date_created":"2019-12-15T23:00:42Z","date_published":"2019-12-01T00:00:00Z","doi":"10.1096/fj.201901543R","page":"13734-13746","publication":"FASEB Journal","day":"01","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"FASEB","file_date_updated":"2020-12-06T17:30:09Z","department":[{"_id":"RySh"}],"ddc":["571","599"],"date_updated":"2023-09-06T14:34:36Z","status":"public","article_type":"original","type":"journal_article","_id":"7179","issue":"12","volume":33,"language":[{"iso":"eng"}],"file":[{"creator":"shigemot","date_updated":"2020-12-06T17:30:09Z","file_size":4766789,"date_created":"2020-12-06T17:30:09Z","file_name":"Klotz et al 2019 EMBO Reports.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"79e3b72481dc32489911121cf3b7d8d0","file_id":"8922","success":1}],"publication_status":"published","publication_identifier":{"eissn":["15306860"]},"intvolume":" 33","month":"12","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity.","lang":"eng"}]},{"publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.08021","open_access":"1"}],"month":"11","date_updated":"2023-09-06T14:37:55Z","department":[{"_id":"DaAl"}],"_id":"7201","type":"conference","conference":{"name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis","end_date":"2019-11-19","location":"Denver, CO, Unites States","start_date":"2019-11-17"},"status":"public","isi":1,"year":"2019","day":"17","publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","date_published":"2019-11-17T00:00:00Z","doi":"10.1145/3295500.3356222","date_created":"2019-12-22T23:00:42Z","quality_controlled":"1","publisher":"ACM","oa":1,"citation":{"mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Cedric","full_name":"Renggli, Cedric","last_name":"Renggli"},{"last_name":"Ashkboos","full_name":"Ashkboos, Saleh","first_name":"Saleh","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A"},{"last_name":"Aghagolzadeh","full_name":"Aghagolzadeh, Mehdi","first_name":"Mehdi"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Hoefler","full_name":"Hoefler, Torsten","first_name":"Torsten"}],"article_processing_charge":"No","external_id":{"isi":["000545976800011"],"arxiv":["1802.08021"]},"title":"SparCML: High-performance sparse communication for machine learning","article_number":"a11","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}]},{"department":[{"_id":"NiBa"}],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK"},"date_updated":"2023-09-06T14:48:57Z","status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"13067","related_material":{"record":[{"id":"7205","status":"public","relation":"used_in_publication"}]},"date_published":"2019-12-02T00:00:00Z","doi":"10.5061/DRYAD.TB2RBNZWK","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:36:27Z","day":"02","year":"2019","month":"12","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}]},{"publication_status":"published","publication_identifier":{"eissn":["14712105"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_BMCBioinfo_Aganezov.pdf","date_created":"2020-01-02T16:10:58Z","creator":"dernst","file_size":1917374,"date_updated":"2020-07-14T12:47:54Z","file_id":"7221","checksum":"7a30357efdcf8f66587ed495c0927724","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"volume":20,"abstract":[{"lang":"eng","text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 20","month":"12","date_updated":"2023-09-06T14:51:06Z","ddc":["570"],"department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:54Z","_id":"7214","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","year":"2019","isi":1,"has_accepted_license":"1","publication":"BMC Bioinformatics","day":"17","date_created":"2019-12-29T23:00:46Z","doi":"10.1186/s12859-019-3208-4","date_published":"2019-12-17T00:00:00Z","oa":1,"publisher":"BMC","quality_controlled":"1","citation":{"mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000511618800007"]},"author":[{"full_name":"Aganezov, Sergey","last_name":"Aganezov","first_name":"Sergey"},{"first_name":"Ilya","last_name":"Zban","full_name":"Zban, Ilya"},{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii"},{"first_name":"Nikita","last_name":"Alexeev","full_name":"Alexeev, Nikita"},{"full_name":"Schatz, Michael C.","last_name":"Schatz","first_name":"Michael C."}],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","article_number":"641"},{"external_id":{"isi":["000505590000024"],"pmid":["31816954"]},"article_processing_charge":"Yes","author":[{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"}],"title":"Frontiers in microfluidics, a teaching resource review","citation":{"ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.","ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","short":"J. Merrin, Bioengineering 6 (2019).","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"109","date_created":"2020-01-05T23:00:45Z","date_published":"2019-12-03T00:00:00Z","doi":"10.3390/bioengineering6040109","year":"2019","has_accepted_license":"1","isi":1,"publication":"Bioengineering","day":"03","oa":1,"quality_controlled":"1","publisher":"MDPI","file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"NanoFab"}],"date_updated":"2023-09-06T14:52:49Z","ddc":["620"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"review","type":"journal_article","status":"public","_id":"7225","volume":6,"issue":"4","publication_status":"published","publication_identifier":{"eissn":["23065354"]},"language":[{"iso":"eng"}],"file":[{"file_size":2660780,"date_updated":"2020-07-14T12:47:54Z","creator":"dernst","file_name":"2019_Bioengineering_Merrin.pdf","date_created":"2020-01-07T14:49:59Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7243","checksum":"80f1499e2a4caccdf3aa54b137fd99a0"}],"scopus_import":"1","intvolume":" 6","month":"12","abstract":[{"lang":"eng","text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications."}],"pmid":1,"oa_version":"Published Version"}]